Do you own the game through Steam or GOG? I think Steam has the option to update the game to the latest version, but if you downloaded the game recently it should already be updated to the latest version, because there hasn't been an update for quite some time now. GOG has patches you can download when clicking on the game in your profile on their website.

The brig door is most likely a case of missed journal entries. You might not have done everything you were supposed to do to get them to open that door for you. You would need to explain in greater detail what you have done, and what you haven't.